feat: update ontologies and add punning term removal for CL (#302)

This pull request introduces several updates to the ontology builder
workflow and associated assets. The most significant change is the
implementation of an automated process to remove "punning" terms from
the CL ontology file using the ROBOT tool in Docker, addressing
compatibility issues with `owlready2`. Additionally, ontology versions
are updated to their latest releases, and the workflow is improved for
consistency and reproducibility.

**Ontology handling improvements:**

* Added a new function `_remove_punning_terms_from_cl` in
`all_ontology_generator.py` to automatically remove punning terms from
the CL ontology file using the ROBOT tool via Docker, ensuring
compatibility with `owlready2` and automating a previously manual step.
* Updated the download logic in `all_ontology_generator.py` to invoke
the punning term removal step after downloading the CL ontology.
* Modified the `Makefile` to pull the required `obolibrary/robot:v1.9.8`
Docker image as part of the install process, ensuring the tool is
available for ontology processing.
* Changed the workflow step in
`.github/workflows/generate_all_ontology.yml` to use `make install`
instead of a direct `pip install`, ensuring all dependencies (including
Docker image) are set up.

**Ontology asset updates:**

* Updated multiple ontology versions and filenames in
`ontology_info.json` to reference the latest releases and correct files
(e.g., CL, EFO, MONDO, NCBITaxon, UBERON, FBbt, FBdv, ZFA, WBls, WBbt,
and HANCESTRO).
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[[2]](diffhunk://#diff-237773e9d64e2aa651a176e2c0e3bb5da1a4edfbf08c8f4ae34228fea1e41148L43-R48)
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[[5]](diffhunk://#diff-237773e9d64e2aa651a176e2c0e3bb5da1a4edfbf08c8f4ae34228fea1e41148L85-R90)

These changes collectively improve the reliability and maintainability
of the ontology builder by automating compatibility fixes and keeping
ontology data up to date.

---------

Co-authored-by: github-actions <[email protected]>

Author: Bento007

.github/workflows/generate_all_ontology.yml

@@ -36,7 +36,7 @@ jobs:
       - name: install requirements
         run: |
           cd tools/ontology-builder
-          pip install -r requirements.txt
+          make install
       - name: setup git
         run: |
           git config user.name github-actions

api/python/ontology-assets-version.txt

@@ -1 +1 @@
-81d9dacfd7f242a17ebd2636598f92ee418e8041
+6feb574af7b4af0fbea6428820648198b1020471